<commit_before>#!/bin/bash -ve


if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi



#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G \
              --left reads.left.fq \
              --right reads.right.fq \
              --SS_lib_type RF \
              --CPU 4 

##### Done Running Trinity #####

if [ $* ]; then
    # check full-length reconstruction stats:
    ./test_FL.sh --query trinity_out_dir/Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse<commit_msg>use the gzipped fq files<commit_after>#!/bin/bash -ve

#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G \
              --left reads.left.fq.gz \
              --right reads.right.fq.gz \
              --SS_lib_type RF \
              --CPU 4 

##### Done Running Trinity #####

if [ $* ]; then
    # check full-length reconstruction stats:
    ./test_FL.sh --query trinity_out_dir/Trinity.fasta --target __indiv_ex_sample_derived/refSeqs.fa --no_reuse
{'fraction_non_alphanumeric': 0.28055555555555556, 'fraction_numerical': 0.002777777777777778, 'mean_word_length': 2.5492610837438425, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6602363', 'n_tokens_mistral': 467, 'n_tokens_neox': 439, 'n_words': 97}