#!/usr/bin/env python
# coding: utf-8

# ## Notebook for getting count matrix for 4 libraries to be used in `DESeq2` from crab transcriptome v 3.1

# #### Based on this notebook from Steven Roberts:  https://github.com/sr320/nb-2020/blob/master/C_bairdi/20-kallisto.ipynb

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get_ipython().system('/Applications/bioinfo/kallisto/kallisto')


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get_ipython().system('pwd')


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ls


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get_ipython().system('wget --no-check-certificate https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v3.1.fasta')


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get_ipython().system('/Applications/bioinfo/kallisto/kallisto  index -i cbai_transcriptome_31  cbai_transcriptome_v3.1.fasta')


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get_ipython().system('/Applications/bioinfo/kallisto/kallisto quant  -i /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/cbai_transcriptome_31  -t 4  -o kallisto/380822_cold_uninfected/  /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380822_S3_L001_R1_001.fastp-trim.202004144409.fq.gz /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380822_S3_L001_R2_001.fastp-trim.202004144409.fq.gz')


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get_ipython().system('/Applications/bioinfo/kallisto/kallisto quant  -i /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/cbai_transcriptome_31  -t 4  -o kallisto/380823_cold_infected/  /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380823_S4_L001_R1_001.fastp-trim.202004144852.fq.gz /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380823_S4_L001_R2_001.fastp-trim.202004144852.fq.gz')


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get_ipython().system('/Applications/bioinfo/kallisto/kallisto quant  -i /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/cbai_transcriptome_31  -t 4  -o kallisto/380824_warm_uninfected/  /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380824_S5_L001_R2_001.fastp-trim.202004145320.fq.gz /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380824_S5_L001_R1_001.fastp-trim.202004145320.fq.gz')


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get_ipython().system('/Applications/bioinfo/kallisto/kallisto quant  -i /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/cbai_transcriptome_31  -t 4  -o kallisto/380825_warm_infected/  /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380825_S6_L001_R1_001.fastp-trim.202004145835.fq.gz /Volumes/web/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/380825_S6_L001_R2_001.fastp-trim.202004145835.fq.gz')


# ### Create matrix

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get_ipython().system('perl /Applications/bioinfo/trinityrnaseq-v2.8.6/util/abundance_estimates_to_matrix.pl')


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get_ipython().system('perl /Applications/bioinfo/trinityrnaseq-v2.8.6/util/abundance_estimates_to_matrix.pl  --est_method kallisto      --gene_trans_map none      --out_prefix /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812      --name_sample_by_basedir       /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380822_cold_uninfected/abundance.tsv       /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380823_cold_infected/abundance.tsv       /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380824_warm_uninfected/abundance.tsv       /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/notebooks/kallisto/380825_warm_infected/abundance.tsv')


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get_ipython().system('head /Users/graciecrandall/Documents/GitHub/paper-tanner-crab/analyses/kallisto-0812/kallisto-0812.isoform.counts.matrix')


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