clust_iden='0.90'
clust_cov="0.50"
consen_iden='0.80'
extra_iden='0.80'
mcl_inflation='1.6'
strict_synt="1"
out_dir_base='out'
pctl_low="25"
pctl_med="50"
pctl_hi="75"
consen_prefix='Zea.pan3'
annot_str_regex='(\D+\d+\D+)\d+.+'
preferred_annot='Zm00001eb'
order_method="reference"
work_dir="/project/maizegdb/ethy/pan-zea-complete/work_pan_zea_Jan_24"
out_dir_base=/project/maizegdb/ethy/pan-zea-complete/pandagma/out_Jan_24

##### (required) list of GFF & FASTA file paths
# Uncomment add file paths to the the annotation_files and fasta_files arrays.
# The nth listed GFF file corresponds to the nth listed FASTA file.

annotation_files=(
  data/Zd-Gigi-REFERENCE-PanAnd-1.0_Zd00001aa.1.gff3.bed.gz
  data/Zd-Momo-REFERENCE-PanAnd-1.0_Zd00003aa.1.gff3.bed.gz
  data/Zh-RIMHU001-REFERENCE-PanAnd-1.0_Zh00001aa.1.gff3.bed.gz
  data/Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.gff3.bed.gz
  data/Zm-B97-REFERENCE-NAM-1.0_Zm00018ab.1.gff3.bed.gz
  data/Zm-CML103-REFERENCE-NAM-1.0_Zm00021ab.1.gff3.bed.gz
  data/Zm-CML228-REFERENCE-NAM-1.0_Zm00022ab.1.gff3.bed.gz
  data/Zm-CML247-REFERENCE-NAM-1.0_Zm00023ab.1.gff3.bed.gz
  data/Zm-CML277-REFERENCE-NAM-1.0_Zm00024ab.1.gff3.bed.gz
  data/Zm-CML322-REFERENCE-NAM-1.0_Zm00025ab.1.gff3.bed.gz
  data/Zm-CML333-REFERENCE-NAM-1.0_Zm00026ab.1.gff3.bed.gz
  data/Zm-CML52-REFERENCE-NAM-1.0_Zm00019ab.1.gff3.bed.gz
  data/Zm-CML69-REFERENCE-NAM-1.0_Zm00020ab.1.gff3.bed.gz
  data/Zm-HP301-REFERENCE-NAM-1.0_Zm00027ab.1.gff3.bed.gz
  data/Zm-Il14H-REFERENCE-NAM-1.0_Zm00028ab.1.gff3.bed.gz
  data/Zm-Ki11-REFERENCE-NAM-1.0_Zm00030ab.1.gff3.bed.gz
  data/Zm-Ki3-REFERENCE-NAM-1.0_Zm00029ab.1.gff3.bed.gz
  data/Zm-Ky21-REFERENCE-NAM-1.0_Zm00031ab.1.gff3.bed.gz
  data/Zm-M162W-REFERENCE-NAM-1.0_Zm00033ab.1.gff3.bed.gz
  data/Zm-M37W-REFERENCE-NAM-1.0_Zm00032ab.1.gff3.bed.gz
  data/Zm-Mo18W-REFERENCE-NAM-1.0_Zm00034ab.1.gff3.bed.gz
  data/Zm-Ms71-REFERENCE-NAM-1.0_Zm00035ab.1.gff3.bed.gz
  data/Zm-NC350-REFERENCE-NAM-1.0_Zm00036ab.1.gff3.bed.gz
  data/Zm-NC358-REFERENCE-NAM-1.0_Zm00037ab.1.gff3.bed.gz
  data/Zm-Oh43-REFERENCE-NAM-1.0_Zm00039ab.1.gff3.bed.gz
  data/Zm-Oh7B-REFERENCE-NAM-1.0_Zm00038ab.1.gff3.bed.gz
  data/Zm-P39-REFERENCE-NAM-1.0_Zm00040ab.1.gff3.bed.gz
  data/Zm-Tx303-REFERENCE-NAM-1.0_Zm00041ab.1.gff3.bed.gz
  data/Zm-Tzi8-REFERENCE-NAM-1.0_Zm00042ab.1.gff3.bed.gz
  data/Zn-PI615697-REFERENCE-PanAnd-1.0_Zn00001aa.1.gff3.bed.gz
  data/Zv-TIL01-REFERENCE-PanAnd-1.0_Zv00001aa.1.gff3.bed.gz
  data/Zv-TIL11-REFERENCE-PanAnd-1.0_Zv00002aa.1.gff3.bed.gz
  data/Zx-TIL18-REFERENCE-PanAnd-1.0_Zx00002aa.1.gff3.bed.gz
  data/Zx-TIL25-REFERENCE-PanAnd-1.0_Zx00003aa.1.gff3.bed.gz
)

cds_files=(
  data/Zd-Gigi-REFERENCE-PanAnd-1.0_Zd00001aa.1.canonical.cds.fa.gz
  data/Zd-Momo-REFERENCE-PanAnd-1.0_Zd00003aa.1.canonical.cds.fa.gz
  data/Zh-RIMHU001-REFERENCE-PanAnd-1.0_Zh00001aa.1.canonical.cds.fa.gz
  data/Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.canonical.cds.fa.gz
  data/Zm-B97-REFERENCE-NAM-1.0_Zm00018ab.1.canonical.cds.fa.gz
  data/Zm-CML103-REFERENCE-NAM-1.0_Zm00021ab.1.canonical.cds.fa.gz
  data/Zm-CML228-REFERENCE-NAM-1.0_Zm00022ab.1.canonical.cds.fa.gz
  data/Zm-CML247-REFERENCE-NAM-1.0_Zm00023ab.1.canonical.cds.fa.gz
  data/Zm-CML277-REFERENCE-NAM-1.0_Zm00024ab.1.canonical.cds.fa.gz
  data/Zm-CML322-REFERENCE-NAM-1.0_Zm00025ab.1.canonical.cds.fa.gz
  data/Zm-CML333-REFERENCE-NAM-1.0_Zm00026ab.1.canonical.cds.fa.gz
  data/Zm-CML52-REFERENCE-NAM-1.0_Zm00019ab.1.canonical.cds.fa.gz
  data/Zm-CML69-REFERENCE-NAM-1.0_Zm00020ab.1.canonical.cds.fa.gz
  data/Zm-HP301-REFERENCE-NAM-1.0_Zm00027ab.1.canonical.cds.fa.gz
  data/Zm-Il14H-REFERENCE-NAM-1.0_Zm00028ab.1.canonical.cds.fa.gz
  data/Zm-Ki11-REFERENCE-NAM-1.0_Zm00030ab.1.canonical.cds.fa.gz
  data/Zm-Ki3-REFERENCE-NAM-1.0_Zm00029ab.1.canonical.cds.fa.gz
  data/Zm-Ky21-REFERENCE-NAM-1.0_Zm00031ab.1.canonical.cds.fa.gz
  data/Zm-M162W-REFERENCE-NAM-1.0_Zm00033ab.1.canonical.cds.fa.gz
  data/Zm-M37W-REFERENCE-NAM-1.0_Zm00032ab.1.canonical.cds.fa.gz
  data/Zm-Mo18W-REFERENCE-NAM-1.0_Zm00034ab.1.canonical.cds.fa.gz
  data/Zm-Ms71-REFERENCE-NAM-1.0_Zm00035ab.1.canonical.cds.fa.gz
  data/Zm-NC350-REFERENCE-NAM-1.0_Zm00036ab.1.canonical.cds.fa.gz
  data/Zm-NC358-REFERENCE-NAM-1.0_Zm00037ab.1.canonical.cds.fa.gz
  data/Zm-Oh43-REFERENCE-NAM-1.0_Zm00039ab.1.canonical.cds.fa.gz
  data/Zm-Oh7B-REFERENCE-NAM-1.0_Zm00038ab.1.canonical.cds.fa.gz
  data/Zm-P39-REFERENCE-NAM-1.0_Zm00040ab.1.canonical.cds.fa.gz
  data/Zm-Tx303-REFERENCE-NAM-1.0_Zm00041ab.1.canonical.cds.fa.gz
  data/Zm-Tzi8-REFERENCE-NAM-1.0_Zm00042ab.1.canonical.cds.fa.gz
  data/Zn-PI615697-REFERENCE-PanAnd-1.0_Zn00001aa.1.canonical.cds.fa.gz
  data/Zv-TIL01-REFERENCE-PanAnd-1.0_Zv00001aa.1.canonical.cds.fa.gz
  data/Zv-TIL11-REFERENCE-PanAnd-1.0_Zv00002aa.1.canonical.cds.fa.gz
  data/Zx-TIL18-REFERENCE-PanAnd-1.0_Zx00002aa.1.canonical.cds.fa.gz
  data/Zx-TIL25-REFERENCE-PanAnd-1.0_Zx00003aa.1.canonical.cds.fa.gz
)

annotation_files_extra_constr=(
  data/Zm-B73-REFERENCE-GRAMENE-3.0_Zm00001c.1.gff3.bed.gz
  data/Zm-A188-REFERENCE-KSU-1.0_Zm00056aa.1.gff3.bed.gz
  data/Zm-A632-REFERENCE-CAAS_FIL-1.0_Zm00092aa.1.gff3.bed.gz
  data/Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.gff3.bed.gz
  data/Zm-Chang-7_2-REFERENCE-CAAS_FIL-1.0_Zm00093aa.1.gff3.bed.gz
  data/Zm-Dan340-REFERENCE-CAAS_FIL-1.0_Zm00094aa.1.gff3.bed.gz
  data/Zm-DK105-REFERENCE-TUM-1.0_Zm00016a.1.gff3.bed.gz
  data/Zm-EP1-REFERENCE-TUM-1.0_Zm00010a.1.gff3.bed.gz
  data/Zm-F7-REFERENCE-TUM-1.0_Zm00011a.1.gff3.bed.gz
  data/Zm-Huangzaosi-REFERENCE-CAAS_FIL-1.0_Zm00095aa.1.gff3.bed.gz
  data/Zm-Ia453-REFERENCE-FL-1.0_Zm00045a.1.gff3.bed.gz
  data/Zm-Jing724-REFERENCE-CAAS_FIL-1.0_Zm00096aa.1.gff3.bed.gz
  data/Zm-Jing92-REFERENCE-CAAS_FIL-1.0_Zm00097aa.1.gff3.bed.gz
  data/Zm-K0326Y-REFERENCE-SIPPE-1.0_Zm00054a.1.gff3.bed.gz
  data/Zm-Mo17-REFERENCE-CAU-2.0_Zm00014ba.gff3.bed.gz
  data/Zm-PE0075-REFERENCE-TUM-1.0_Zm00017a.1.gff3.bed.gz
  data/Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0_Zm00008a.1.gff3.bed.gz
  data/Zm-S37-REFERENCE-CAAS_FIL-1.0_Zm00100aa.1.gff3.bed.gz
  data/Zm-SK-REFERENCE-YAN-1.0_Zm00015a.1.gff3.bed.gz
  data/Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.gff3.bed.gz
  data/Zm-Xu178-REFERENCE-CAAS_FIL-1.0_Zm00101aa.1.gff3.bed.gz
  data/Zm-Ye478-REFERENCE-CAAS_FIL-1.0_Zm00102aa.1.gff3.bed.gz
  data/Zm-Zheng58-REFERENCE-CAAS_FIL-1.0_Zm00103aa.1.gff3.bed.gz
)

cds_files_extra_constr=(
  data/Zm-B73-REFERENCE-GRAMENE-3.0_Zm00001c.1.canonical.cds.fa.gz
  data/Zm-A188-REFERENCE-KSU-1.0_Zm00056aa.1.canonical.cds.fa.gz
  data/Zm-A632-REFERENCE-CAAS_FIL-1.0_Zm00092aa.1.canonical.cds.fa.gz
  data/Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.canonical.cds.fa.gz
  data/Zm-Chang-7_2-REFERENCE-CAAS_FIL-1.0_Zm00093aa.1.canonical.cds.fa.gz
  data/Zm-Dan340-REFERENCE-CAAS_FIL-1.0_Zm00094aa.1.canonical.cds.fa.gz
  data/Zm-DK105-REFERENCE-TUM-1.0_Zm00016a.1.canonical.cds.fa.gz
  data/Zm-EP1-REFERENCE-TUM-1.0_Zm00010a.1.canonical.cds.fa.gz
  data/Zm-F7-REFERENCE-TUM-1.0_Zm00011a.1.canonical.cds.fa.gz
  data/Zm-Huangzaosi-REFERENCE-CAAS_FIL-1.0_Zm00095aa.1.canonical.cds.fa.gz
  data/Zm-Ia453-REFERENCE-FL-1.0_Zm00045a.1.canonical.cds.fa.gz
  data/Zm-Jing724-REFERENCE-CAAS_FIL-1.0_Zm00096aa.1.canonical.cds.fa.gz
  data/Zm-Jing92-REFERENCE-CAAS_FIL-1.0_Zm00097aa.1.canonical.cds.fa.gz
  data/Zm-K0326Y-REFERENCE-SIPPE-1.0_Zm00054a.1.canonical.cds.fa.gz
  data/Zm-Mo17-REFERENCE-CAU-2.0_Zm00014ba.canonical.cds.fa.gz
  data/Zm-PE0075-REFERENCE-TUM-1.0_Zm00017a.1.canonical.cds.fa.gz
  data/Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0_Zm00008a.1.canonical.cds.fa.gz
  data/Zm-S37-REFERENCE-CAAS_FIL-1.0_Zm00100aa.1.canonical.cds.fa.gz
  data/Zm-SK-REFERENCE-YAN-1.0_Zm00015a.1.canonical.cds.fa.gz
  data/Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.canonical.cds.fa.gz
  data/Zm-Xu178-REFERENCE-CAAS_FIL-1.0_Zm00101aa.1.canonical.cds.fa.gz
  data/Zm-Ye478-REFERENCE-CAAS_FIL-1.0_Zm00102aa.1.canonical.cds.fa.gz
  data/Zm-Zheng58-REFERENCE-CAAS_FIL-1.0_Zm00103aa.1.canonical.cds.fa.gz
)

annotation_files_extra_free=(
)

cds_files_extra_free=(
)

protein_files=(
  data/Zd-Gigi-REFERENCE-PanAnd-1.0_Zd00001aa.1.protein.fa.gz
  data/Zd-Momo-REFERENCE-PanAnd-1.0_Zd00003aa.1.protein.fa.gz
  data/Zh-RIMHU001-REFERENCE-PanAnd-1.0_Zh00001aa.1.protein.fa.gz
  data/Zm-A188-REFERENCE-KSU-1.0_Zm00056aa.1.protein.fa.gz
  data/Zm-A632-REFERENCE-CAAS_FIL-1.0_Zm00092aa.1.protein.fa.gz
  data/Zm-B73-REFERENCE-GRAMENE-3.0_Zm00001c.1.protein.fa.gz
  data/Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.protein.fa.gz
  data/Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.fa.gz
  data/Zm-B97-REFERENCE-NAM-1.0_Zm00018ab.1.protein.fa.gz
  data/Zm-Chang-7_2-REFERENCE-CAAS_FIL-1.0_Zm00093aa.1.protein.fa.gz
#  data/Zm-CIMBL55-REFERENCE-CAU-1.0_Zm00067a.1.protein.fa.gz
  data/Zm-CML103-REFERENCE-NAM-1.0_Zm00021ab.1.protein.fa.gz
  data/Zm-CML228-REFERENCE-NAM-1.0_Zm00022ab.1.protein.fa.gz
  data/Zm-CML247-REFERENCE-NAM-1.0_Zm00023ab.1.protein.fa.gz
  data/Zm-CML277-REFERENCE-NAM-1.0_Zm00024ab.1.protein.fa.gz
  data/Zm-CML322-REFERENCE-NAM-1.0_Zm00025ab.1.protein.fa.gz
  data/Zm-CML333-REFERENCE-NAM-1.0_Zm00026ab.1.protein.fa.gz
  data/Zm-CML52-REFERENCE-NAM-1.0_Zm00019ab.1.protein.fa.gz
  data/Zm-CML69-REFERENCE-NAM-1.0_Zm00020ab.1.protein.fa.gz
  data/Zm-Dan340-REFERENCE-CAAS_FIL-1.0_Zm00094aa.1.protein.fa.gz
  data/Zm-DK105-REFERENCE-TUM-1.0_Zm00016a.1.protein.fa.gz
  data/Zm-EP1-REFERENCE-TUM-1.0_Zm00010a.1.protein.fa.gz
  data/Zm-F7-REFERENCE-TUM-1.0_Zm00011a.1.protein.fa.gz
  data/Zm-HP301-REFERENCE-NAM-1.0_Zm00027ab.1.protein.fa.gz
  data/Zm-Huangzaosi-REFERENCE-CAAS_FIL-1.0_Zm00095aa.1.protein.fa.gz
  data/Zm-Ia453-REFERENCE-FL-1.0_Zm00045a.1.protein.fa.gz
  data/Zm-Il14H-REFERENCE-NAM-1.0_Zm00028ab.1.protein.fa.gz
  data/Zm-Jing724-REFERENCE-CAAS_FIL-1.0_Zm00096aa.1.protein.fa.gz
  data/Zm-Jing92-REFERENCE-CAAS_FIL-1.0_Zm00097aa.1.protein.fa.gz
  data/Zm-K0326Y-REFERENCE-SIPPE-1.0_Zm00054a.1.protein.fa.gz
  data/Zm-Ki11-REFERENCE-NAM-1.0_Zm00030ab.1.protein.fa.gz
  data/Zm-Ki3-REFERENCE-NAM-1.0_Zm00029ab.1.protein.fa.gz
  data/Zm-Ky21-REFERENCE-NAM-1.0_Zm00031ab.1.protein.fa.gz
  data/Zm-M162W-REFERENCE-NAM-1.0_Zm00033ab.1.protein.fa.gz
  data/Zm-M37W-REFERENCE-NAM-1.0_Zm00032ab.1.protein.fa.gz
  data/Zm-Mo17-REFERENCE-CAU-2.0_Zm00014ba.protein.fa.gz
  data/Zm-Mo18W-REFERENCE-NAM-1.0_Zm00034ab.1.protein.fa.gz
  data/Zm-Ms71-REFERENCE-NAM-1.0_Zm00035ab.1.protein.fa.gz
  data/Zm-NC350-REFERENCE-NAM-1.0_Zm00036ab.1.protein.fa.gz
  data/Zm-NC358-REFERENCE-NAM-1.0_Zm00037ab.1.protein.fa.gz
  data/Zm-Oh43-REFERENCE-NAM-1.0_Zm00039ab.1.protein.fa.gz
  data/Zm-Oh7B-REFERENCE-NAM-1.0_Zm00038ab.1.protein.fa.gz
  data/Zm-P39-REFERENCE-NAM-1.0_Zm00040ab.1.protein.fa.gz
  data/Zm-PE0075-REFERENCE-TUM-1.0_Zm00017a.1.protein.fa.gz
  data/Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0_Zm00008a.1.protein.fa.gz
  data/Zm-S37-REFERENCE-CAAS_FIL-1.0_Zm00100aa.1.protein.fa.gz
  data/Zm-SK-REFERENCE-YAN-1.0_Zm00015a.1.protein.fa.gz
  data/Zm-Tx303-REFERENCE-NAM-1.0_Zm00041ab.1.protein.fa.gz
  data/Zm-Tzi8-REFERENCE-NAM-1.0_Zm00042ab.1.protein.fa.gz
  data/Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.fa.gz
  data/Zm-Xu178-REFERENCE-CAAS_FIL-1.0_Zm00101aa.1.protein.fa.gz
  data/Zm-Ye478-REFERENCE-CAAS_FIL-1.0_Zm00102aa.1.protein.fa.gz
  data/Zm-Zheng58-REFERENCE-CAAS_FIL-1.0_Zm00103aa.1.protein.fa.gz
  data/Zn-PI615697-REFERENCE-PanAnd-1.0_Zn00001aa.1.protein.fa.gz
  data/Zv-TIL01-REFERENCE-PanAnd-1.0_Zv00001aa.1.protein.fa.gz
  data/Zv-TIL11-REFERENCE-PanAnd-1.0_Zv00002aa.1.protein.fa.gz
  data/Zx-TIL18-REFERENCE-PanAnd-1.0_Zx00002aa.1.protein.fa.gz
  data/Zx-TIL25-REFERENCE-PanAnd-1.0_Zx00003aa.1.protein.fa.gz
)

#### (optional) expected_chr_matches file path
expected_chr_matches='data/expected_chr_matches.tsv'